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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
ccafc2de5a
Workflow run template was causing these methods to be called wrong (and has been for a LONG time), this in turn caused me to misunderstand what the spec for how other_values in tool parameters should operate when writing the tests. The real underlying bug should be fixed with 55cf8bb.
108 lines
5.1 KiB
Python
108 lines
5.1 KiB
Python
from unittest import TestCase
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from galaxy.util import bunch
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from galaxy import model
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from galaxy.tools.parameters import basic
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from elementtree.ElementTree import XML
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import tools_support
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class SelectToolParameterTestCase( TestCase, tools_support.UsesApp ):
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def test_dep_dummy_datasets_need_late_validation( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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assert self.param.need_late_validation( self.trans, { "input_bam": basic.DummyDataset() } )
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def test_dep_runtime_values_need_late_validation( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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assert self.param.need_late_validation( self.trans, { "input_bam": basic.RuntimeValue() } )
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def test_dep_unvalidated_values_need_late_validation( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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assert self.param.need_late_validation( self.trans, { "input_bam": basic.UnvalidatedValue( "42" ) } )
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def test_dep_real_datasets_no_late_validation( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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assert not self.param.need_late_validation( self.trans, { "input_bam": model.HistoryDatasetAssociation() } )
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def test_nested_context_validation_needed( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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# Data ref currently must be same level, if not at top level.
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assert self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": basic.RuntimeValue() } } )
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def test_nested_context_validation_not_needed( self ):
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self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
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# Data ref currently must be same level, if not at top level.
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assert not self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } } )
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def test_filter_param_value( self ):
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self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''
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assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, { "input_bam": "testname1" } )
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assert ("testname2", "testpath2", False) in self.param.get_options( self.trans, { "input_bam": "testname2" } )
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assert len( self.param.get_options( self.trans, { "input_bam": "testname3" } ) ) == 0
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def test_filter_param_value2( self ):
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# Same test as above, but filtering on a different column.
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self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>'''
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assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, { "input_bam": "testpath1" } )
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assert ("testname2", "testpath2", False) in self.param.get_options( self.trans, { "input_bam": "testpath2" } )
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assert len( self.param.get_options( self.trans, { "input_bam": "testpath3" } ) ) == 0
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# TODO: Good deal of overlap here with DataToolParameterTestCase,
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# refactor.
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def setUp( self ):
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self.setup_app( mock_model=False )
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self.mock_tool = bunch.Bunch(
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app=self.app,
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tool_type="default",
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)
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self.test_history = model.History()
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self.app.model.context.add( self.test_history )
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self.app.model.context.flush()
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self.app.tool_data_tables[ "test_table" ] = MockToolDataTable()
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self.trans = bunch.Bunch(
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app=self.app,
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get_history=lambda: self.test_history,
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get_current_user_roles=lambda: [],
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workflow_building_mode=False,
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webapp=bunch.Bunch( name="galaxy" ),
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)
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self.type = "select"
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self.set_data_ref = False
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self.multiple = False
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self.optional = False
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self.options_xml = ""
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self._param = None
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@property
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def param( self ):
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if not self._param:
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multi_text = ""
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if self.multiple:
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multi_text = 'multiple="True"'
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optional_text = ""
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if self.optional:
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optional_text = 'optional="True"'
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options_text = self.options_xml
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data_ref_text = ""
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if self.set_data_ref:
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data_ref_text = 'data_ref="input_bam"'
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template_xml = '''<param name="my_name" type="%s" %s %s %s>%s</param>'''
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self.param_xml = XML( template_xml % ( self.type, data_ref_text, multi_text, optional_text, options_text ) )
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self._param = basic.SelectToolParameter( self.mock_tool, self.param_xml )
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return self._param
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class MockToolDataTable( object ):
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def __init__( self ):
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self.columns = dict(
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name=0,
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value=1,
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)
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self.missing_index_file = None
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def get_fields( self ):
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return [ [ "testname1", "testpath1" ], [ "testname2", "testpath2" ] ]
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